HEADER TRANSCRIPTION 29-JUN-18 6DXO TITLE 1.8 A STRUCTURE OF RSBN-BLDN COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE ECF-SUBFAMILY SIGMA FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BLDN; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE (STRAIN ATCC 10712 / SOURCE 3 CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745); SOURCE 4 ORGANISM_TAXID: 953739; SOURCE 5 STRAIN: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 SOURCE 6 / PD 04745; SOURCE 7 GENE: SVEN_3185; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE (STRAIN ATCC 10712 / SOURCE 12 CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745); SOURCE 13 ORGANISM_TAXID: 953739; SOURCE 14 STRAIN: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 SOURCE 15 / PD 04745; SOURCE 16 GENE: SVEN_3186; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BLDN, RSBN, SIGMA, ANTI-SIGMA, ECF, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 3 11-OCT-23 6DXO 1 REMARK REVDAT 2 05-SEP-18 6DXO 1 JRNL REVDAT 1 11-JUL-18 6DXO 0 SPRSDE 11-JUL-18 6DXO 6C03 JRNL AUTH M.A.SCHUMACHER,M.J.BUSH,M.J.BIBB,F.RAMOS-LEON,G.CHANDRA, JRNL AUTH 2 W.ZENG,M.J.BUTTNER JRNL TITL THE CRYSTAL STRUCTURE OF THE RSBN-SIGMA BLDN COMPLEX FROM JRNL TITL 2 STREPTOMYCES VENEZUELAE DEFINES A NEW STRUCTURAL CLASS OF JRNL TITL 3 ANTI-SIGMA FACTOR. JRNL REF NUCLEIC ACIDS RES. V. 46 7405 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29905823 JRNL DOI 10.1093/NAR/GKY493 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.770 REMARK 3 COMPLETENESS FOR RANGE (%) : 77.5 REMARK 3 NUMBER OF REFLECTIONS : 29209 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.0617 - 3.8725 0.54 1845 184 0.2257 0.2271 REMARK 3 2 3.8725 - 3.0760 0.76 2618 268 0.1791 0.2141 REMARK 3 3 3.0760 - 2.6879 0.80 2717 280 0.1931 0.2352 REMARK 3 4 2.6879 - 2.4424 0.81 2780 274 0.1988 0.2533 REMARK 3 5 2.4424 - 2.2675 0.81 2780 281 0.1987 0.2457 REMARK 3 6 2.2675 - 2.1339 0.81 2769 274 0.1969 0.2416 REMARK 3 7 2.1339 - 2.0271 0.81 2768 268 0.2042 0.2466 REMARK 3 8 2.0271 - 1.9389 0.81 2759 275 0.2097 0.2310 REMARK 3 9 1.9389 - 1.8643 0.80 2770 264 0.2377 0.2800 REMARK 3 10 1.8643 - 1.8000 0.80 2777 258 0.2732 0.3246 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.45 REMARK 3 B_SOL : 71.06 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.81620 REMARK 3 B22 (A**2) : -4.07780 REMARK 3 B33 (A**2) : 10.89400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.96940 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1566 REMARK 3 ANGLE : 0.898 2114 REMARK 3 CHIRALITY : 0.061 243 REMARK 3 PLANARITY : 0.004 275 REMARK 3 DIHEDRAL : 13.424 576 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -5.5551 0.5690 24.9492 REMARK 3 T TENSOR REMARK 3 T11: 0.1343 T22: 0.1070 REMARK 3 T33: 0.1232 T12: -0.0002 REMARK 3 T13: -0.0050 T23: 0.0314 REMARK 3 L TENSOR REMARK 3 L11: 1.3907 L22: 1.1169 REMARK 3 L33: 0.8459 L12: 0.8989 REMARK 3 L13: -0.0433 L23: 0.9491 REMARK 3 S TENSOR REMARK 3 S11: -0.0142 S12: 0.0441 S13: -0.0897 REMARK 3 S21: -0.0790 S22: 0.1143 S23: -0.1357 REMARK 3 S31: -0.0194 S32: 0.0692 S33: 0.0012 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DXO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.01 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29209 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 23.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13600 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6C03 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE, 26% PEG 3500, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.68750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PHE A 107 REMARK 465 LYS A 108 REMARK 465 SER A 109 REMARK 465 MET A 110 REMARK 465 GLU A 111 REMARK 465 SER A 112 REMARK 465 LEU A 113 REMARK 465 PRO A 173 REMARK 465 ASP A 174 REMARK 465 ASP A 175 REMARK 465 ALA A 176 REMARK 465 ARG A 177 REMARK 465 MET D 1 REMARK 465 GLU D 22 REMARK 465 SER D 23 REMARK 465 GLU D 24 REMARK 465 GLY D 25 REMARK 465 ALA D 26 REMARK 465 ALA D 27 REMARK 465 ALA D 28 REMARK 465 GLU D 29 REMARK 465 GLN D 30 REMARK 465 THR D 31 REMARK 465 GLU D 32 REMARK 465 THR D 33 REMARK 465 THR D 34 REMARK 465 ALA D 35 REMARK 465 GLU D 36 REMARK 465 PRO D 37 REMARK 465 ALA D 38 REMARK 465 GLU D 80 REMARK 465 GLY D 81 REMARK 465 SER D 82 REMARK 465 ALA D 83 REMARK 465 ALA D 84 REMARK 465 ALA D 85 REMARK 465 ALA D 86 REMARK 465 PRO D 87 REMARK 465 THR D 88 REMARK 465 VAL D 89 REMARK 465 PRO D 90 REMARK 465 GLU D 91 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 2 N CG OD1 OD2 REMARK 470 ILE D 2 CG1 CG2 CD1 REMARK 470 GLU D 39 CG CD OE1 OE2 REMARK 470 MET D 79 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 145 CD GLU A 145 OE2 0.076 REMARK 500 REMARK 500 REMARK: NULL DBREF 6DXO A 1 177 PDB 6DXO 6DXO 1 177 DBREF 6DXO D 1 91 UNP F2R912 F2R912_STRVP 1 91 SEQRES 1 A 151 MET ASP LEU VAL ASP ARG ALA GLN ALA GLY GLU ALA GLU SEQRES 2 A 151 ALA PHE GLY ARG LEU TYR ASP GLN TYR SER ASP THR VAL SEQRES 3 A 151 TYR ARG TYR ILE TYR TYR ARG VAL GLY GLY LYS ALA THR SEQRES 4 A 151 ALA GLU ASP LEU THR SER GLU THR PHE LEU ARG ALA LEU SEQRES 5 A 151 ARG ARG ILE SER THR PHE THR TRP GLN GLY ARG ASP PHE SEQRES 6 A 151 GLY ALA TRP LEU VAL THR ILE ALA ARG ASN LEU VAL ALA SEQRES 7 A 151 ASP HIS PHE LYS SER MET GLU SER LEU SER ASN ALA ALA SEQRES 8 A 151 LEU LEU ASP ALA VAL ARG ARG LEU ASN PRO GLN GLN GLN SEQRES 9 A 151 GLU CYS VAL THR LEU ARG PHE LEU GLN GLY LEU SER VAL SEQRES 10 A 151 ALA GLU THR ALA ARG VAL MET GLY LYS ASN GLU GLY ALA SEQRES 11 A 151 ILE LYS THR LEU GLN TYR ARG ALA VAL ARG THR LEU ALA SEQRES 12 A 151 ARG LEU LEU PRO ASP ASP ALA ARG SEQRES 1 D 91 MET ILE ALA ASN VAL SER ALA HIS ARG ARG ALA ASN ALA SEQRES 2 D 91 PHE ALA GLN ALA LEU GLU ASP ARG GLU SER GLU GLY ALA SEQRES 3 D 91 ALA ALA GLU GLN THR GLU THR THR ALA GLU PRO ALA GLU SEQRES 4 D 91 GLN GLY LYS LEU LEU ALA LEU ALA SER GLY LEU GLY ASP SEQRES 5 D 91 LEU PRO LYS PRO GLN LEU ASP PRO GLU VAL LYS VAL VAL SEQRES 6 D 91 GLN ARG ALA GLN LEU VAL ALA ALA MET GLU ALA MET LEU SEQRES 7 D 91 MET GLU GLY SER ALA ALA ALA ALA PRO THR VAL PRO GLU FORMUL 3 HOH *135(H2 O) HELIX 1 AA1 ASP A 2 GLN A 8 1 7 HELIX 2 AA2 GLU A 11 TYR A 32 1 22 HELIX 3 AA3 GLY A 36 ARG A 54 1 19 HELIX 4 AA4 ASP A 64 HIS A 80 1 17 HELIX 5 AA5 ASN A 115 LEU A 125 1 11 HELIX 6 AA6 ASN A 126 LEU A 138 1 13 HELIX 7 AA7 SER A 142 GLY A 151 1 10 HELIX 8 AA8 ASN A 153 LEU A 171 1 19 HELIX 9 AA9 ALA D 3 ARG D 21 1 19 HELIX 10 AB1 GLN D 40 ASP D 52 1 13 HELIX 11 AB2 ASP D 59 MET D 79 1 21 CRYST1 44.409 43.375 58.715 90.00 111.97 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022518 0.000000 0.009083 0.00000 SCALE2 0.000000 0.023055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018365 0.00000